diff readme @ 0:efd9c309b8f7

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readme	Tue Mar 26 14:50:53 2013 -0400
@@ -0,0 +1,165 @@
+OSRA: Optical Structure Recognition Application
+
+OSRA is a utility designed to convert graphical representations of chemical 
+structures, as they appear in journal articles, patent documents, textbooks, 
+trade magazines etc., into SMILES (Simplified Molecular Input Line Entry 
+Specification - see http://en.wikipedia.org/wiki/SMILES) or 
+SD files - a computer recognizable molecular structure format. 
+OSRA can read a document in any of the over 90 graphical formats parseable by 
+ImageMagick - including GIF, JPEG, PNG, TIFF, PDF, PS etc., and generate 
+the SMILES or SDF representation of the molecular structure images encountered 
+within that document.
+
+Note that any software designed for optical recognition is unlikely to be 
+perfect, and the output produced might, and probably will, contain errors, 
+so curation by a human knowledgeable in chemical structures is highly recommended.
+
+http://cactus.nci.nih.gov/osra/
+
+
+The wrapper comes with an automatic installation of all dependencies through the
+galaxy toolshed. If you do not want to use that feature you can compile OSRA with
+the following instructions.
+
+
+########################################
+#                                      #
+#           OSRA Setup                 #
+# currently a small patch is requiered #
+#                                      #
+########################################
+
+Save the following file to 'osra-1.4.0-configure.patch' and store it next 
+to that script below.
+
+-------------------------------------------------------
+--- configure	2013-03-18 18:14:00.888605219 +0100
++++ configure_ori	2013-03-18 18:13:48.396605759 +0100
+@@ -4178,7 +4178,8 @@
+ 
+ # Check whether --with-tclap-include was given.
+ if test "${with_tclap_include+set}" = set; then :
+-  withval=$with_tclap_include;
++    withval=$with_tclap_include;
++    CPPFLAGS="-I${withval} ${CPPFLAGS}"
+ else
+   with_tclap_include="auto"
+ fi
+-------------------------------------------------------
+
+#!/usr/bin/bash
+#osra installation
+
+cdir=`pwd`
+
+wget http://sourceforge.net/projects/graphicsmagick/files/graphicsmagick/1.3.18/GraphicsMagick-1.3.18.tar.gz
+tar xfvz GraphicsMagick-1.3.18.tar.gz
+cd GraphicsMagick-1.3.18
+./configure --prefix=`pwd`/build --enable-shared=yes
+make
+make install
+cd ..
+
+export PATH=$PATH:/home/bag/projects/osra/GraphicsMagick-1.3.18/build/bin/
+
+wget http://potrace.sourceforge.net/download/potrace-1.11.tar.gz
+tar xfvz potrace-1.11.tar.gz
+cd potrace-1.11
+./configure --with-libpotrace --prefix=`pwd`/build
+make
+make install
+cd ..
+
+wget http://downloads.sourceforge.net/project/osra/gocr-patched/gocr-0.50pre-patched.tgz
+tar xfvz gocr-0.50pre-patched.tgz
+cd gocr-0.50pre-patched
+./configure --prefix=`pwd`/build
+make libs
+make all install
+cd ..
+
+wget http://downloads.sourceforge.net/project/tclap/tclap-1.2.1.tar.gz
+tar xfvz tclap-1.2.1.tar.gz
+cd tclap-1.2.1
+./configure --prefix=`pwd`/build
+make
+make install
+cd ..
+
+wget http://mirror.checkdomain.de/gnu/ocrad/ocrad-0.21.tar.gz
+tar xfvz ocrad-0.21.tar.gz
+cd ocrad-0.21
+./configure --prefix=`pwd`/build
+make
+make install
+cd ..
+
+wget http://downloads.sourceforge.net/project/openbabel/openbabel/2.3.2/openbabel-2.3.2.tar.gz
+tar xfvz openbabel-2.3.2.tar.gz
+cd openbabel-2.3.2
+mkdir build
+cd build
+cmake .. -DCMAKE_INSTALL_PREFIX=`pwd`/install/
+make
+make install
+cd ../..
+
+#wget http://tesseract-ocr.googlecode.com/files/tesseract-ocr-3.02.02.tar.gz
+#tar xfvz tesseract-ocr-3.02.02.tar.gz
+#cd tesseract-ocr
+#./configure --prefix=`pwd`/build
+#make
+#make install
+#cd ..
+
+
+wget https://launchpad.net/cuneiform-linux/1.1/1.1/+download/cuneiform-linux-1.1.0.tar.bz2
+tar xfvj cuneiform-linux-1.1.0.tar.bz2
+cd cuneiform-linux-1.1.0
+mkdir build
+cd build
+cmake .. -DCMAKE_INSTALL_PREFIX=`pwd`/install/
+make
+make install
+cd ../..
+
+
+wget http://downloads.sourceforge.net/project/osra/osra/1.4.0/osra-1.4.0.tgz
+tar xfvz osra-1.4.0.tgz
+patch osra-1.4.0/configure < osra-1.4.0-configure.patch
+cd osra-1.4.0
+
+./configure --with-tclap-include=$cdir/tclap-1.2.1/build/include/ \
+--with-potrace-include=$cdir/potrace-1.11/build/include/ \
+--with-potrace-lib=$cdir/potrace-1.11/build/lib/ \
+--with-gocr-include=$cdir/gocr-0.50pre-patched/build/include/gocr/ \
+--with-gocr-lib=$cdir/gocr-0.50pre-patched/build/lib/ \
+--with-ocrad-include=$cdir/ocrad-0.21/build/include/ \
+--with-ocrad-lib=$cdir/ocrad-0.21/build/lib/ \
+--with-cuneiform-include=$cdir/cuneiform-linux-1.1.0/build/install/include/ \
+--with-cuneiform \
+--with-cuneiform-lib=$cdir/cuneiform-linux-1.1.0/build/install/lib/ \
+--with-openbabel-include=$cdir/openbabel-2.3.2/build/install/include/openbabel-2.0/ \
+--with-openbabel-lib=$cdir/openbabel-2.3.2/build/install/lib/ \
+--with-graphicsmagick-lib=$cdir/GraphicsMagick-1.3.18/build/lib/ \
+--with-graphicsmagick-include=$cdir/GraphicsMagick-1.3.18/build/include/GraphicsMagick/ \
+--prefix=`pwd`/bin/ 
+#--enable-static-linking --disable-graphicsmagick-config
+make
+make install
+
+export LD_LIBRARY_PATH=$cdir/GraphicsMagick-1.3.18/build/lib/:$cdir/GraphicsMagick-1.3.18/build/lib:$cdir/potrace-1.11/build/lib/
+./bin/bin/osra
+
+
+#--with-tesseract-include=$cdir/tclap-1.2.1/build/include/
+#--with-tesseract
+#--with-tesseract-lib
+
+
+
+
+
+
+
+